BCL7A

BAF chromatin remodeling complex subunit BCL7A, the group of BAF complex

Basic information

Region (hg38): 12:122019421-122062044

Previous symbols: [ "BCL7" ]

Links

ENSG00000110987 ∙ NCBI:605 ∙ OMIM:601406 ∙ HGNC:1004 ∙ Uniprot:Q4VC05 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BCL7A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCL7A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in BCL7A

This is a list of pathogenic ClinVar variants found in the BCL7A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-122043960-G-A		not specified	Uncertain significance (Aug 15, 2023)
12-122044006-A-G		not specified	Uncertain significance (Nov 15, 2021)
12-122044033-A-G		not specified	Uncertain significance (Jul 12, 2023)
12-122054853-A-G		not specified	Uncertain significance (Sep 30, 2021)
12-122054883-C-G		BCL7A-related disorder	Likely benign (Jun 05, 2023)
12-122054933-C-G		not specified	Uncertain significance (Nov 15, 2021)
12-122054967-G-A		not specified	Uncertain significance (Apr 27, 2023)
12-122054976-T-C		not specified	Uncertain significance (Nov 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCL7A	protein_coding	protein_coding	ENST00000538010	6	42621

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0782	0.912	125718	0	7	125725	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.898	113	143	0.789	0.00000833	1519
Missense in Polyphen		31	50.615	0.61246		594
Synonymous	-0.132	60	58.7	1.02	0.00000422	434
Loss of Function	2.25	4	12.6	0.317	7.34e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=Chromosomal aberrations involving BCL7A may be a cause of B-cell non-Hodgkin lymphoma. Three-way translocation t(8;14;12)(q24.1;q32.3;q24.1) with MYC and with immunoglobulin gene regions. {ECO:0000269|PubMed:8605326}.
• Pathway: TNFalpha (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.379
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.121
• hipred: Y
• hipred_score: 0.640
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.405

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Bcl7a
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of transcription, DNA-templated
• Cellular component: cellular_component
• Molecular function: molecular_function;protein binding